2R2L

Structure of Farnesyl Protein Transferase bound to PB-93


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Efficacy, pharmacokinetics, and metabolism of tetrahydroquinoline inhibitors of Plasmodium falciparum protein farnesyltransferase.

Van Voorhis, W.C.Rivas, K.L.Bendale, P.Nallan, L.Horney, C.Barrett, L.K.Bauer, K.D.Smart, B.P.Ankala, S.Hucke, O.Verlinde, C.L.Chakrabarti, D.Strickland, C.Yokoyama, K.Buckner, F.S.Hamilton, A.D.Williams, D.K.Lombardo, L.J.Floyd, D.Gelb, M.H.

(2007) Antimicrob Agents Chemother 51: 3659-3671

  • DOI: https://doi.org/10.1128/AAC.00246-07
  • Primary Citation of Related Structures:  
    2R2L

  • PubMed Abstract: 

    New antimalarials are urgently needed. We have shown that tetrahydroquinoline (THQ) protein farnesyltransferase (PFT) inhibitors (PFTIs) are effective against the Plasmodium falciparum PFT and are effective at killing P. falciparum in vitro. Previously described THQ PFTIs had limitations of poor oral bioavailability and rapid clearance from the circulation of rodents. In this paper, we validate both the Caco-2 cell permeability model for predicting THQ intestinal absorption and the in vitro liver microsome model for predicting THQ clearance in vivo. Incremental improvements in efficacy, oral absorption, and clearance rate were monitored by in vitro tests; and these tests were followed up with in vivo absorption, distribution, metabolism, and excretion studies. One compound, PB-93, achieved cure when it was given orally to P. berghei-infected rats every 8 h for a total of 72 h. However, PB-93 was rapidly cleared, and dosing every 12 h failed to cure the rats. Thus, the in vivo results corroborate the in vitro pharmacodynamics and demonstrate that 72 h of continuous high-level exposure to PFTIs is necessary to kill plasmodia. The metabolism of PB-93 was demonstrated by a novel technique that relied on double labeling with a radiolabel and heavy isotopes combined with radiometric liquid chromatography and mass spectrometry. The major liver microsome metabolite of PB-93 has the PFT Zn-binding N-methyl-imidazole removed; this metabolite is inactive in blocking PFT function. By solving the X-ray crystal structure of PB-93 bound to rat PFT, a model of PB-93 bound to malarial PFT was constructed. This model suggests areas of the THQ PFTIs that can be modified to retain efficacy and protect the Zn-binding N-methyl-imidazole from dealkylation.


  • Organizational Affiliation

    Department of Medicine, University of Washington, Room I-104-E, Health Sciences Building, Seattle, WA 98195-7185, USA. wesley@u.washington.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyltransferase subunit alpha315Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyltransferase subunit beta401Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02293
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PB9
Query on PB9

Download Ideal Coordinates CCD File 
E [auth B]methyl 4-{[{(3S)-6-cyano-1-[(1-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroquinolin-3-yl}(pyridin-2-ylsulfonyl)amino]methyl}piperidine-1-carboxylate
C28 H33 N7 O4 S
BRIVIXLMMUIBJY-DEOSSOPVSA-N
FPP
Query on FPP

Download Ideal Coordinates CCD File 
D [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP BindingDB:  2R2L Kd: 2 (nM) from 1 assay(s)
PB9 BindingDB:  2R2L IC50: 3.2 (nM) from 1 assay(s)
PDBBind:  2R2L IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.614α = 90
b = 171.614β = 90
c = 69.155γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations